If anything, Ben's moral stance should be stronger than Peter's. Ben, after all, didn't have it constantly tested by Green Goblins, Sin-Eaters, etc.
That's true, eh? He was the one who had to calm Peter down when he was on the verge of a nervous breakdown.
He did play fast and loose with the law in other ways, lying about his credentials and identity to get jobs. The only time I could see him actually crossing a line like that was before he met Seward Trainer, when he was homeless, friendless, depressed, and possibly near-suicidal...
But even then... a lot of scenes from that era have him getting angry and breaking something or threatening someone, and then cursing Peter's upbringing for making him incapable of that kind of violence.
He was simultaneously more innocent and more mature than Peter Parker. He'd seen more of the world, dealt with poverty and loneliness, and basically had to rely on himself (whereas Peter could almost always count on Aunt May, MJ, or his friends). At the same time, he wasn't constantly faced with criminals and people who wanted him dead; he didn't have to deal with most of the real horrors Peter had to.
I'll give Guggenheim a tiny bit of benefit of the doubt and assume he means the characters might think he'd done it.